I am making a PBBG (persistant browser based game) which is a small multiplayer RPG. I am facing a small dichotomy:

1) I want to have a singleplayer storyline that explores the human condition, like for example "30 flights of loving". This would require fixed characters and events.

2) At the same time, this is going to be a multiplayer game where players get to customize their character, and have to player with many others like them.

How would I reconcile this? Are there examples of this being done? While a singleplayer mode is one solution, I am hoping not to integrate the story itself into the multiplayer. Perhaps the player can discover pieces/remains of the story through notes and diaries while going through the multiplayer map?

Bioshock used multiple tape recorders to tell several different stories to great effect. Numerous games have used notes/diaries to similar purposes. Portal used Graffiti "There is no cake" . So there are a number of delivery systems you could implement.

You might consider also the use of a timed delivery system i.e. as time passes in the world you might have pieces of the story dropped into it. Possibly 2 people communicating through graffiti. And as you play the game for longer - new pieces of graffiti appears - a form of star -crossed lovers separated by the circumstances of the zombies....could even have them arrange to meet but something goes wrong i.e. another human attempting to grab the girl and her writing of this after she had failed to appear. Shouldn't be too hard to map out an entire story that way and just have the game drop in the pieces at appropriate trigger.

If you have dungeons, you could use NPCs and props specific to one dungeon to tell a short story - Skyrim has several examples. Or the opposite direction, you could make story quests not be tied to any location, but instead part of the GUI/menu system, such that players could pursue them in between group activities. It would not have to be a full single player mode, but solo quests that could be accomplished while others were nearby without disrupting the group play with them too much.

I want to help design a "sandpark" MMO. Optional interactive story with quests and deeply characterized NPCs, plus sandbox elements like player-craftable housing and lots of other crafting. If you are starting a design of this type, please PM me. I also love pet-breeding games.

You might wanna check how Guild Wars 2 did it: when creating the character, they give the player a choice of a few parameters. Like how rich their family was or what is their biggest fear. Then you get a story that depends on your race and these few choices you had. With like 6 parameters for each race, you get a lot of storyline variants. They are still pretty obvious, but it brings some variety. Story is told in instances and when you enter these instances, people can accompany you. If they are in the same story moment and are currently following the same storyline, they can progress their story with you. Of course, it has lots of problems, like repeating the same story elements, killing the same NPC multiple times with different parties, etc. Still, a nice step forward in terms of storytelling in multiplayer.

After reading them and thinking about it for a while, I am considering having players view/discover the story via journals/tapes/graffiti and instanced dungeons as they explore (if they chooses) the game world.

To entice people to actually do this, and to provide a guide, this might be given as a "story quest" or an achievement to unlock, with a set of objectives that lead players through the story.